[chimerax-users] Color protein by residue

[Tom Goddard]

Hi Tom,

  We use Vive and Oculus Rift with ChimeraX to display structures and microscopy data (the “vr” command).  I am interested in how you have used VR to look at PDB models.  Can you tell me more?

	Tom


> On Aug 28, 2017, at 11:27 AM, Tom Skillman  wrote:
> 
> Hi Elaine,
>  
> I guess I was asking both questions: 1) Is it possible to color a PDB protein by residue, i.e. each of the 23 residues as a different, but consistent, color across the whole protein, and 2) Do you support any of the standard color schemes like this one that I've used in the past – 
>  
> <image002.jpg>
>  
> I'm more interested in the first issues - can I color ByResidue (with any color scheme)?   J
>  
> Thanks for your assistance.
>  
> Best,
> Tom
>  
> Thomas Skillman
> Director Research Technology
> Benaroya Research Institute for Autoimmune Disease
> Seattle, WA
>  
> PS – If you are interested, I created an VR based immersive space for collaborating on PDB models. It adds another dimension to looking at and discussing protein structure.  Let me know if you’re interested and we can set up a time to give you a demo.
>  
>  
>  
>  
> -----Original Message-----
> From: Elaine Meng 
> Sent: Monday, August 28, 2017 9:59 AM
> To: Tom Skillman 
> Cc: chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Color protein by residue
>  
> Hi Tom,
> I don’t know what you mean by standard colors.  There is “color byelement” for using element color-coding of atoms, “color byhet” for leaving carbons unchanged and element color-coding the other atoms.  The element colors are shown here:
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#element <http://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#element>>
>  
> There is no set of standard colors indicating the amino acid types, if that’s what you meant, at least not in ChimeraX.  That may be the reason you couldn’t figure it out.  :-)
>  
> I hope this clarifies,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>  
>  
> > On Aug 27, 2017, at 8:30 PM, Tom Skillman  wrote:
> > 
> > I can’t figure out the command for coloring the proteins of a protein with standard colors.. Can you help?  Thx.
>  
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